Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge

Thomas C Terwilliger; Paul D Adams; Pavel V Afonine; Oleg V Sobolev

doi:10.1016/j.jsb.2018.07.016

Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge

J Struct Biol. 2018 Nov;204(2):338-343. doi: 10.1016/j.jsb.2018.07.016. Epub 2018 Jul 29.

Authors

Thomas C Terwilliger¹, Paul D Adams², Pavel V Afonine³, Oleg V Sobolev⁴

Affiliations

¹ Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87544, USA. Electronic address: tterwilliger@newmexicoconsortium.org.
² Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA.
³ Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA; Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China.
⁴ Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA.

Abstract

A recently-developed method for identifying a compact, contiguous region representing the unique part of a density map was applied to 218 Cryo-EM maps with resolutions of 4.5 Å or better. The key elements of the segmentation procedure are (1) identification of all regions of density above a threshold and (2) choice of a unique set of these regions, taking symmetry into consideration, that maximize connectivity and compactness. This segmentation approach was then combined with tools for automated map sharpening and model-building to generate models for the 12 maps in the 2016 Cryo-EM Model Challenge in a fully automated manner. The resulting models have completeness from 24% to 82% and RMS distances from reference interpretations of 0.6 Å-2.1 Å.

Keywords: Electron cryo-microscopy; Map segmentation; Model-building.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Cryoelectron Microscopy / methods*
Protein Conformation
Protein Structure, Secondary

Grants and funding

P01 GM063210/GM/NIGMS NIH HHS/United States